Manouvering below the MSA in climb is the responsibility of the pilot.... much like when we give a departure clearance.... we don't turn aircraft until they're at the minimum vectoring altitude... what pilots do, their business... we do, if the weather is really poor, use the phrase "at safe altitude left/right turn....", if feeling the pilots may not know the area we may even draw the attention to the MSA.
We, as you state, do not have complete radarcoverage, and an aircraft comming in via the fiord with mountains on both sides cannot be seen at 500' until 10 miles out. If such an aircraft is given 5300' (MSA) we make sure we have procedural (non radar) separation to all other flights, until he shows up on radar. That could mean stop departures, and stop descends at 6300'...
If the situation for the VFR fligth is not critical, we'll wait until there is room, if it is critical, we'll MAKE room
It's generally not rocket science, but do understand your own responsibility in this matter, we have had too many accidents over the years where a crew thought ATC had responsibility.
EDIT: I just forgot something: "Clearances are issued solely for expediting and separating air traffic and are based on known traffic conditions
which affect safety in aircraft operation".... straight out of DOC4444